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opencc-zeroAug 2020View details →

Footprints of local adaptation span hundreds of linked genes in the Atlantic silverside genome

The study of local adaptation in the presence of ongoing gene flow is the study of natural selection in action, revealing the functional genetic diversity most relevant to contemporary pressures. In addition to individual genes, genome-wide architecture can itself evolve to enable adaptation. Distributed across a steep thermal gradient along the east coast of North America, Atlantic silversides (Menidia menidia) exhibit an extraordinary degree of local adaptation in a suite of traits, and the capacity for rapid adaptation from standing genetic variation, but we know little about the patterns of genomic variation across the species range that enable this remarkable adaptability. Here we use low-coverage, whole-transcriptome sequencing of Atlantic silversides sampled along an environmental cline to show marked signatures of divergent selection across a gradient of neutral differentiation. Atlantic silversides sampled across 1,371 km of the southern section of its distribution have very low genome-wide differentiation (median FST=0.006 across 1.9 million variants), consistent with historical connectivity and observations of recent migrants. Yet almost 14,000 single nucleotide polymorphisms (SNPs) are nearly fixed (FST>0.95) for alternate alleles. Highly differentiated SNPs cluster into four tight linkage disequilibrium blocks (LD) that span hundreds of genes and several megabases. Variants in these LD blocks are disproportionately non-synonymous and concentrated in genes enriched for multiple functions related to known adaptations in silversides, including variation in lipid storage, metabolic rate, and spawning behavior. Elevated levels of absolute divergence and demographic modeling suggest selection maintaining divergence across these blocks under gene flow. These findings represent an extreme case of heterogeneity in levels of differentiation across the genome, and highlight how gene flow shapes genomic architecture in continuous populations. Locally adapted alleles may be common features of populations distributed along environmental gradients, and will likely be key to conserving variation to enable future responses to environmental change.

opencc-zeroDec 2023View details →

Data from: Temperature-dependent gene regulatory divergence underlies local adaptation with gene flow in the Atlantic silverside

<p>Gene regulatory divergence is thought to play an important role in adaptation, yet its extent and underlying mechanisms remain largely elusive for local adaptation with gene flow. Local adaptation is widespread in marine species despite generally high connectivity and is often associated with tightly linked genomic architectures, such as chromosomal inversions. To investigate gene regulatory evolution under gene flow and the role of inversions associated with local adaptation to a steep thermal gradient, we generated RNA-seq data from Atlantic silversides (<em>Menidia menidia</em>) from two locally adapted populations and their F1 hybrids, reared under two temperatures. We found substantial divergence in gene expression and thermal plasticity between populations, with up to 31% of genes being differentially expressed. Reduced thermal plasticity, temperature-dependent gene misexpression and the disruption of co-expression networks in hybrids point towards a role of regulatory incompatibilities in local adaptation, particularly under colder temperatures. Chromosomal inversions show an accumulation of regulatory incompatibilities but are not consistently enriched for differentially expressed genes. Together, these results suggest that gene regulation can diverge substantially among populations despite gene flow, partly due to the accumulation of temperature-dependent regulatory incompatibilities within inversions.</p>

publicMar 2024View details →

Data from: Temperature-dependent gene regulatory divergence underlies local adaptation with gene flow in the Atlantic silverside

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publicAug 2020View details →

Footprints of local adaptation span hundreds of linked genes in the Atlantic silverside genome

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FIGURE 5 in Two new miniature silverside fishes of the genus Membras Bonaparte (Atheriniformes, Atherinopsidae) from the Tropical North Atlantic Ocean

FIGURE 5. Shape space: principal components of Procrustes-aligned, scale-adjusted shape space (= relative warps); 99% confidence limits shown for each species, the dots indicate the centroid value for each species; the dashed line in the Membras martinica ellipse demarcates the area of the ellipse occupied by individuals less than 45 mm SL. The ellipses are: 1 Membras martinca; 2 M. analis; 3 M. dissimilis; 4. M. procera sp. nov.; 5 M. argentea; 6 M. pygmaea sp. nov.

FIGURE 2 in Two new miniature silverside fishes of the genus Membras Bonaparte (Atheriniformes, Atherinopsidae) from the Tropical North Atlantic Ocean

FIGURE 2. Map of Honduras to northern Colombia showing the localities for Membras pygmaea sp. nov., Brus Lagoon, Honduras and M. procera sp. nov., Gulf of Urabá, Colombia.

FIGURE 4 in Two new miniature silverside fishes of the genus Membras Bonaparte (Atheriniformes, Atherinopsidae) from the Tropical North Atlantic Ocean

FIGURE 4. Outline of Membras pygmaea sp. nov., showing the landmarks that were digitized. The dashed line on the ventral side indicates the location of the anal pore. The digitized landmarks: 1 tip of snout; 2 posterior margin of occiput; 3 origin of spinous dorsal fin; 4 origin of second dorsal fin; 5 terminus of second dorsal fin; 6 posterior margin of hypural plate; 7 terminus of anal fin; 8 origin of anal fin; 9 insertion of pelvic fin; 10 posterior bony margin of head; 11 insertion of pectoral fin; 12 posterior extent of gular region; 13 posterior margin of orbit; 14 anterior margin of orbit; 15 posterior margin of upper jaw.

FIGURE 1 in Two new miniature silverside fishes of the genus Membras Bonaparte (Atheriniformes, Atherinopsidae) from the Tropical North Atlantic Ocean

FIGURE 1. Map of southern Central America and South America showing the distribution of the miniature species of the Membras martinica species-group as follows: (i) star—M. pygmaea sp. nov., Brus Lagoon, Honduras; (ii) triangle—M. procera sp. nov., Gulf of Urabá, Colombia; (iii) circle—M. argentea, off Sabanilla, Colombia; (iv) arrow—M. analis, off Lago Maracaibo, Venezuela; and (v) square—M. dissimilis, off Cananéia, Brazil.

FIGURE 3. A in Two new miniature silverside fishes of the genus Membras Bonaparte (Atheriniformes, Atherinopsidae) from the Tropical North Atlantic Ocean

FIGURE 3. A. Membras pygmaea sp. nov., holotype, FMNH 117282, 40.2 mm SL. B. Membras procera sp. nov., holotype, ANSP 153427, 36.6 mm SL.

FIGURE 6 in Two new miniature silverside fishes of the genus Membras Bonaparte (Atheriniformes, Atherinopsidae) from the Tropical North Atlantic Ocean

FIGURE 6. Deformation grids among landmarks for the shape space in Figure 5. The vectors coming off the grids indicate: i) the magnitude of the changes such that individuals with higher scores (to the right of PC1 or the top of PC2) are enlarged morphologically; and ii) the directions of the displacement of the landmarks.